Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021593.1 Corchorus olitorius cultivar O-4 contig21626, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 6164
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:1298 original size:18 final size:17

Alignment explanation


    Indices: 1275--1312  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       1265 CCCAAATTAC

                              
       1275 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       1293 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       1310 TTA
          1 TTA

       1313 AATAAATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32


Consensus pattern (17 bp):   
TTATGGAAATTAGGAAA

Found at i:1310 original size:8 final size:9

Alignment explanation


    Indices: 1279--1312  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       1269 AATTACTTAT

                     
       1279 GGAAATTAG
          1 GGAAATTAG

                    *
       1288 GGAAATTAT
          1 GGAAATTAG

                     
       1297 GGAAATTA-
          1 GGAAATTAG

                    
       1305 GGAAATTA
          1 GGAAATTA

       1313 AATAAATTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8    8  0.33
   9   16  0.67

ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26


Consensus pattern (9 bp):   
GGAAATTAG

Found at i:2667 original size:49 final size:47

Alignment explanation


    Indices: 2590--2730  Score: 151
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       2580 CAAGCAACCC

                *      *                                    
       2590 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                     *                          * *        *  
       2638 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGAAAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                        *         *                      
       2687 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       2731 TTGGCACGCT


Statistics
Matches: 77,  Mismatches: 11, Indels: 11
        0.78            0.11        0.11

Matches are distributed among these distances:
  47   14  0.18
  48   22  0.29
  49   34  0.44
  50    7  0.09

ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50


Consensus pattern (47 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:2870 original size:21 final size:22

Alignment explanation


    Indices: 2846--2890  Score: 56
    Period size: 24  Copynumber: 2.0  Consensus size: 22

       2836 TTGTAAAGAT

                         *        
       2846 ATTAGA-TTTAGTTGAATAAAA
          1 ATTAGATTTTAGTAGAATAAAA

                                    
       2867 ATTAGAGTTTTTAGTAGAATAAAA
          1 ATTAGA--TTTTAGTAGAATAAAA

       2891 CTATAATAGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  21    6  0.30
  24   14  0.70

ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38


Consensus pattern (22 bp):   
ATTAGATTTTAGTAGAATAAAA
Done.